Martin,
I checked out my toppie on the Port of Melbourne web cam during the worst of the blow, and I can reassure you that the moored boats were coping a pounding - the wind was recorded at 57.2 knots! (that is in excess of 106 km per hour).
I saw my boat get hit side on by a very strong gust and whilst it didn't lay her over, it did make it heel to about 30 degrees. Perhaps if your storm boards were not sealing properly, these could have let in some water during the heeling - may be worth checking along with your cockpit drains to see if they are blocked.
Cheers,
Kevin
Wayward Lady, a Mark 111
Williamstown, Vic